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WO2009030780A2 - Echafaudage protéique non naturel constitué de trois peptides associés de manière non covalente - Google Patents

Echafaudage protéique non naturel constitué de trois peptides associés de manière non covalente Download PDF

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Publication number
WO2009030780A2
WO2009030780A2 PCT/EP2008/061886 EP2008061886W WO2009030780A2 WO 2009030780 A2 WO2009030780 A2 WO 2009030780A2 EP 2008061886 W EP2008061886 W EP 2008061886W WO 2009030780 A2 WO2009030780 A2 WO 2009030780A2
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residues
amino acid
peptides
scaffold
peptide
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PCT/EP2008/061886
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WO2009030780A3 (fr
Inventor
Johan Desmet
Ignace Lasters
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Complix Nv
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Priority to EP08803854A priority Critical patent/EP2188303B1/fr
Priority to US12/676,783 priority patent/US9217011B2/en
Priority to AT08803854T priority patent/ATE538129T1/de
Publication of WO2009030780A2 publication Critical patent/WO2009030780A2/fr
Publication of WO2009030780A3 publication Critical patent/WO2009030780A3/fr

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K1/00—General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/001—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof by chemical synthesis
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K7/00—Peptides having 5 to 20 amino acids in a fully defined sequence; Derivatives thereof
    • C07K7/04—Linear peptides containing only normal peptide links
    • C07K7/08—Linear peptides containing only normal peptide links having 12 to 20 amino acids
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2318/00—Antibody mimetics or scaffolds
    • C07K2318/20—Antigen-binding scaffold molecules wherein the scaffold is not an immunoglobulin variable region or antibody mimetics

Definitions

  • the present invention is in the field of molecular biology and is related to a non-natural and thermodynamically stable proteinaceous (or protein) scaffold consisting of three non- covalently associated peptides.
  • This scaffold presenting possible therapeutic, diagnostic or purification purposes, can be used in the field of drug discovery, analytical research, purification technology and as a model for improving research and development of proteinaceous scaffold structures.
  • Molecular compounds that are able to bind proteinaceous target molecules such as flexible peptides in solution, peptides immobilized onto a solid support, linear peptide fragments in a protein, or folded proteins have a broad spectrum of possible applications. For example, they are inherently suited to be used as therapeutic compounds (e.g., inhibitors), detection probes (e.g., detection of a recombinant protein) and purification probes (e.g., in affinity chromatography) . In view of the continuous evolution in these areas, there is an ongoing need for new compounds that can bind specific target molecules .
  • therapeutic compounds e.g., inhibitors
  • detection probes e.g., detection of a recombinant protein
  • purification probes e.g., in affinity chromatography
  • Proteinaceous (protein-like) molecular compounds may fold into triple-stranded, parallel, alpha-helical coiled coil complexes in solution. Such complexes can be very stable and are tolerant to amino acid substitutions. Accordingly, they meet the basic requirements of a protein-based scaffold. Protein- based scaffold molecules are often considered as the 'next- generation' class of compounds for molecular recognition, which increasingly compete with immunoglobulin-based compounds. Compounds of the present invention offer an alternative approach to immunoglobulins, and an additional type of protein-based (proteinaceous) scaffold.
  • Coiled coil complexes have found various applications in the medical and biotechnological fields (e.g., as gene regulators, antibody stabilizers, anticancer drugs, purification tags, hydrogels) .
  • the usage of two-stranded coiled coil scaffolds has been proposed for the construction of combinatorial libraries and for vaccine design.
  • the present invention does not relate to two-stranded coiled coils, nor to combinatorial libraries, nor to vaccine design.
  • the compounds of the present invention are triple-stranded coiled coils; all scaffold molecules used to date are single-stranded or, exceptionally, two-stranded.
  • the triple-stranded alpha- helical coiled coil scaffold of the invention further shows a unique feature: it possesses a highly designable groove in between each pair of interacting alpha-helices.
  • the present invention discloses that the latter feature makes this type of scaffold well-suited for binding to peptidic target compounds. Since the development of peptide-binding molecules is generally known as a difficult problem, the present invention discloses a valuable, innovative and non-obvious alternative to existing approaches.
  • the present invention is related to a non-natural, thermodynamically stable, proteinaceous scaffold consisting of three non-covalently associated peptides, wherein each peptide comprises less than 50 amino acid residues and wherein at least 50% , 55%, 65%, 70%, 75% of the said residues are substitutable into at least 10 different amino acid residue types .
  • the proteinaceous scaffold of the present invention consists of three peptide sequences, wherein each peptide sequence comprises between 2 and 7 consecutive heptad repeats of the formula cxxcxxx, wherein the characters "c" and
  • x denote respectively "core” and "non-core” amino acid residues and wherein the said peptide sequences have the following cumulative properties: a) at least 50% of the c-residues are isoleucine (ILE) amino acid residues, the remaining c-residues being natural or non-natural amino acid residues other than isoleucine (ILE) and proline (PRO); b) each x-residue is an alanine (ALA) amino acid residue; c) the said peptide sequences associate into trimers by way of their heptad repeats forming triple-stranded, parallel, alpha-helical coiled coils wherein the said c- residues form the core; d) (possibly) the coiled coil-forming peptide sequences remain associated under physical conditions that are different from physiological conditions being a pH of 7, a temperature of 37°C and an ionic strength of 0.15 molar; and e) (possibly) each
  • one or more of the c-residues are amino acids selected from the group consisting of valine, leucine, methionine, phenylalanine, tyrosine, tryptophan, histidine, glutamine, threonine, serine, alanine or glycine (or a derivative thereof) or, alternatively, from the group consisting of valine, leucine or methionine (or a derivative thereof) .
  • at least 70%, or, alternatively, at least 90% or, alternatively, all, or all except one, of the c-residues are isoleucines .
  • the peptide sequences remain associated under physical conditions that differ by at least two pH units
  • a factor two (preferably a factor four) in ionic strength from the physiological conditions being a pH of 7, a temperature of 37 °C and an ionic strength of 0.15 molar.
  • the invention further discloses embodiments wherein these peptide sequences comprise two consecutive heptad repeats having the amino acid sequence of SEQ ID NO: 1 : IAAIAAAIAAIAAA or, alternatively, SEQ ID NO: 2 : IAAIQKQIAAIQKQ, or SEQ ID NO : 3 : IAAIAAAIAAIAAAIAAIAAA, or SEQ ID NO : 4 : IAAIQKQIAAIQKQIAAIQKQ .
  • the invention further discloses embodiments wherein the peptide sequences comprise either the amino acid sequence SEQ ID NO: 1: IAAIAAAIAAIAAA or SEQ ID NO : 2 : IAAIQKQIAAIQKQ or SEQ ID NO: 3: IAAIAAAIAAIAAAIAAIAAA or SEQ ID NO:
  • the invention further discloses embodiments wherein these peptides sequences bind to a non-immunoglobulin target compound, said binding being characterized by a dissociation constant Kd lower than 1000 micromolar, preferably lower than 100 micromolar, more preferably lower than 10 micromolar or lower than 1 micromolar.
  • the invention is also related to a method for obtaining the scaffold of the invention, the said method comprising the following steps: a) designing a specific amino acid sequence for the said peptides by applying the following rules: i) the said amino acid sequence comprises consecutive heptad repeats of the formula cxxcxxx, the characters "c" and "x" refering to
  • each x-residue is an alanine amino acid residue; b) producing the designed peptides by chemical synthesis; c) demonstrating that the designed and produced peptides, when brought into solution, associate into trimers by way of their heptad repeats forming triple-stranded, parallel, alpha-helical coiled coils, and wherein the C- residues constitute the core; and demonstrating that the coiled coil-forming peptides remain associated under physical conditions that are different from physiological conditions being a pH of 7, a temperature of 37 °C and an i
  • Non-covalent interactions of proteins with other molecules are at the basis of all biological processes. These interactions determine the strength and specificity of molecular recognition events. Accordingly, rational application of the principles behind such interactions, in combination with biotechnological methods, may provide a means to interfere
  • the present artificial (non-natural, designed) , stable (stably folded, stably associated) scaffold molecules are composed of exactly three individual, non-covalently associated peptide fragments .
  • scaffolds complexes, peptidic associations, also referred to, in more general terms, as molecular compounds
  • thermodynamically stable, thermally stable, chemically stable, pH-insensitive three-dimensional fold (3-D fold, 3-D structure) .
  • amino acids amino acid residues, residues
  • mutated, changed, varied amino acids
  • Scaffold molecules of the invention can be mutated so as to allow them to bind (bind to, bind with) specific target molecules, but one can exactly identify which amino acid residues can (and which cannot) be varied for this purpose.
  • the scaffold molecules (molecular compounds) of the invention are able to interfere with (influence, modify) biological processes through impeding (blocking, inhibiting) natural chemical reactions or natural molecular recognition events, or through creation of non-natural molecular recognition events.
  • Some aspects of the present invention relate to methods to generate or optimize such compounds possibly to detect molecular compounds of interest in a study sample and possibly to isolate molecular compounds of interest from this study sample .
  • Instances of biological interference include, without limitation, blocking of human receptors, binding to pathogenic species, and binding to disease- or disorder-related proteins. Such type of biological interference is typically intended to curate severe diseases or disorders. These applications belong to the field of therapeutic research and development.
  • probe molecules include, without limitation, experimental analyses of samples of human, animal, plant, bacterial, viral, biotechnological or synthetic origin.
  • samples typically contain biomolecules (e.g., polypeptides, polynucleotides, polysaccharides, hormones, vitamins or lipids, or derivatives thereof) that can interact specifically with a selected probe molecule. The latter interaction typically gives rise to a characteristic
  • ligand molecules include, without limitation, samples of human, animal, plant, bacterial, viral, biotechnological or synthetic origin containing biomolecules
  • purification methods include affinity chromatography and immunoprecipitation .
  • desired physico- chemical properties e.g., specificity, affinity, stability, solubility
  • Immunoglobulin molecules are widely used in all of the aforementioned fields. They can recognize a diverse repertoire of target antigens and bind with great specificity.
  • the present invention contemplates the use of a specific type of protein (proteinaceous) scaffold and corresponding specific molecular compounds with binding specificities comparable to those of immunoglobulins, but with a totally distinct composition and structure, and lacking some of the immunoglobulins' weaknesses.
  • ⁇ scaffold' is used within the context of the present invention to denote ⁇ a specific, conformationally (structurally) and thermodynamically (thermally and chemically) stable proteinaceous (protein-like or protein) molecule with a specific, fixed (invariable, invariant) three- dimensional (3-D, tertiary) structure (spatial arrangement of constituting elements) consisting of one or more protein or proteinaceous polypeptide chains, the said structure being demonstrably tolerant to a variety of single and multiple amino acid substitutions at a variety of amino acid residue positions' , where ⁇ tolerant' is to be understood in the sense that the integrity (correctness) of the structure remains essentially unaltered upon performing said amino acid substitutions .
  • Non-immunoglobulin protein-based (proteinaceous) scaffold molecules are considered in the field as a ⁇ next-generation' class of compounds for molecular recognition. They are mostly derived from natural protein molecules which have been selected on basis of preferred physico-chemical properties and available experimental data. Examples of this class of compounds are listed in [Hosse et al . Protein Sci 2006, 15:14- 27] . Protein-based scaffold molecules consist of a stable framework structure (scaffold structure) and one or more regions that can be varied by amino acid substitution (variable regions) without compromising folding of the framework.
  • Appropriate selection methods can be applied for the purpose of identifying variants (scaffold derivatives, specific molecular compounds) with highly desired binding properties (e.g., affinities and specificities) similar to immunoglobulins.
  • Protein-based scaffold molecules have been ascribed numerous advantages over immunoglobulins including, for example, their relatively small size, high structural stability and absence of post-translational modifications. These features considerably facilitate their synthesis, purification and storage.
  • high-affinity compounds can be generated without the need to proceed via an immunization step.
  • One aspect of the present invention relates to a particular type of protein-based scaffold that is relatively insensitive to substitution of surface residues and standard protein engineering actions. Another aspect relates to scaffold- derived compounds, including compounds that tightly bind peptides comprising a sequence pattern of interest.
  • Yet another aspect relates to scaffold-derived compounds, including compounds that tightly bind proteins comprising a surface pattern of interest. All embodiments of the present invention relate to a specific type of protein structure (fold) that has so far not been exploited as a highly mutatable scaffold.
  • Synthetic peptides form a distinct class of non-natural biomolecules that are useful (used) to generate high-affinity and high-specificity binders to selected target molecules.
  • libraries of synthetic peptides can be applied, with variable success, to screen for small peptidic compounds with desired binding properties.
  • flexible synthetic peptides include, without limitation, random or semi-random
  • biasing peptide libraries that are fused (covalently attached) to the N- or C-terminus of a selected carrier protein, peptides known as aptamers (i.e., peptides discovered through a genetic selection technique) , variable heavy chain CDR3-derived peptide libraries, crypteins (i.e., peptides derived from proteolytic fragments of natural proteins) , partially (locally) constrained peptide libraries (e.g., through a pair of disulfide-bonding cysteines), and the like.
  • Peptides (and libraries thereof) that are inserted as loops (i.e., via both their termini) into a scaffold structure of choice are herein considered as belonging to the class of scaffold-based compounds described supra; when such peptides are excised (extracted, isolated) from their scaffold context, they are again considered as free, synthetic peptides.
  • synthetic peptides lack the conformational restraints exerted by protein frameworks (e.g., scaffold structures) . Accordingly, the present invention only remotely relates to the class of synthetic peptides.
  • the peptides forming objects of the present invention demonstrably fold into a specific, well-defined tertiary structure, this property allowing to distinguish them from conformationally flexible peptides and partially (locally) constrained peptides.
  • the alpha-helical (alpha-helical) coiled coil forms a special type of 3-D structural framework (structural motif, fold) .
  • the coiled coil fold occurs in a wide variety of proteins including motor proteins, DNA-binding proteins, extracellular proteins and viral fusion proteins [Burkhard et al . Trends Cell Biol 2001, 11:82-88] .
  • Coiled coils have been functionally characterized as folding (assembly, oligomerization) motifs, i.e., formation of a coiled coil structure drives in many instances the non- covalent association of different protein chains.
  • Coiled coils have been structurally characterized as 2-, 3-, 4- or 5-stranded assemblies of alpha-helices arranged in parallel, anti-parallel or mixed topologies [Lupas Trends Biochem Sci 1996, 21:375-382] .
  • the helices are slightly wrapped (coiled) around each other in a left-handed manner, termed supercoiling .
  • Alpha-helical coiled coils have been further characterized at the level of their amino acid sequences in that each helix is constituted of a series of heptad repeats.
  • a heptad repeat (heptad unit, heptad) is a 7-residue sequence motif which can be encoded as HppHppp, and wherein each H represents a (potentially different) hydrophobic residue (mostly Leu, lie or VaI) and each p is a (potentially different) polar residue (e.g., Ser, Thr, Asn, GIn, Asp, GIu, His, Arg or Lys) . Occasionally (infrequently) , p-residues are observed at H-positions, and vice versa. Coiled coils have been thermodynamically characterized as follows.
  • hydrophobic residues (H) form a hydrophobic seam
  • polar residues (p) form a polar face.
  • the hydrophobic seams of different alpha- helices when associated into a coiled coil, form a central hydrophobic core (center, interior, inner part) . Formation of this core, in combination with orientation of the polar faces toward solvent, is assumed to provide the main thermodynamic driving force required for stable association, although certain non-core residues may enhance stability as well.
  • the present invention also relates to polypeptide sequences
  • polypeptides, peptides, peptide fragments, peptide chains presenting some properties as the full length molecules of the invention comprising multiple heptad repeat motifs.
  • These embodiments further relate to triple-stranded (3-stranded, trimeric) , parallel, alpha-helical coiled coil structures, preferably to stable association of the polypeptide chains in 3-stranded parallel alpha-helical coiled coil structures and to coiled coils for which the core residues provide the main driving force for stable association.
  • Alpha-helical coiled coils have found widespread applications in the medical and biotechnological fields. They have been exploited to function as temperature-sensing gene regulators
  • US Patent No 5,824,483 has claimed the usage of a combinatorial library of conformationally restricted peptides, wherein the said peptides associate (fold) into an alpha- helical coiled coil dimer.
  • Peptide sequences of the scaffold are designed such that they simultaneously fulfill a double role: (i) a subset of the composing amino acid residues, denoted invariant residues, is selected for (serves to) stabilize the dimeric coiled coil, this subset including both amino acid residues suitable to form the hydrophobic core (center, interior) of the coiled coil dimer, and residues that form a covalent intrachain bond (i.e., a covalent bond between residues in one of the constituting peptides, effective to stabilize that peptide in its alpha-helical conformation) , and
  • a subset of the composing amino acid residues, denoted variant residues, is selected among the solvent-exposed residues, and is varied (substituted, mutated) so as to create a unique variation of amino acid residues in the exposed region of at least one of the constituting peptides, this variation involving at least 1000 library members.
  • the inventors essentially claimed a combinatorial library that is based on a dimeric (2-stranded) alpha-helical coiled coil scaffold.
  • the present invention relate to the usage of a trimeric (3-stranded) alpha-helical coiled coil scaffold, and not to coiled coil dimers .
  • the referenced invention US Patent No 5,824,483
  • Trimeric (3-stranded) alpha-helical coiled coils are less frequently observed in natural proteins than are dimeric coiled coils [Wolf et al . Protein Science 1997, 6:1179-1189] .
  • Trimeric coiled coils are also less frequently used for biotechnical or medical purposes [Mason and Arndt ChemBioChem 2004, 5:170-176] .
  • probes ligands, e.g., agonists, antagonists, inverse agonists, inhibitors, detection probes, purification probes, diagnostic probes, etc.
  • their intrinsic scaffold properties in the sense of ⁇ a stably folded structural unit able to carry other elements' , has been exploited almost exclusively under the form of fusion constructs (fusion proteins) .
  • trimeric coiled coil peptides were fused (covalently attached, coupled, linked) to peptides with low trimerization propensity in order to enhance trimerization [Eckert and Kim Proc Natl Acad Sci USA 201, 98: 11187-11192], or coupled to already trimeric complexes in order to further enhance stability of the complex [Yin et al. Nature 2006, 439:38-44] .
  • Dimeric coiled coils are also known to be tolerant to sequence variation (mutations) at the level of their solvent-exposed residues.
  • coiled coil molecules may be useful as scaffold molecules being tolerant to a variety of single and multiple substitutions.
  • coiled coil molecules may be useful as scaffold molecules that can be converted, by way of substitution of the non-core residues, into molecular compounds (ligands) that bind to target molecules of high value in the fields of therapeutics, diagnostics or purification technology.
  • HIV-I envelope glycoprotein gpl ⁇ O
  • HIV-I Env spikes are displayed on the viral surface as trimers of non-covalently associated heterodimers of gpl20 (SU, surface glycoprotein) and gp41 (TM, transmembrane glycoprotein) .
  • X-ray crystallography of the gp41 ectodomain, and smaller (e.g., proteolytic) fragments thereof, has revealed that gp41 can undergo large conformational transitions from a prefusion, via an intermediate (also termed ⁇ pre-hairpin' ) to a postfusion structure.
  • the proteolytically and thermally stable portion of gp41 in its postfusion state has been characterized as a 6-helix bundle with the formula
  • HRl-linker-HR2 3 , where HRl (HR-N, N-helix, N36) represents an
  • HR2 (HR-C, C-helix, C34) represents a
  • each C-helix is linked to the end of an N-helix via a hairpin- forming linker fragment, and binds in an antiparallel orientation onto a groove formed by two adjacent central N- helices .
  • the full 6-helix bundle basically consists of a central trimeric coiled coil, onto which three outer C-helices are packed.
  • the crystallographically determined structures suggest that this type of association is highly specific [Chan et al . Cell 1997, 89:263-273] .
  • Thermal denaturation experiments also suggest that this type of association is fairly stable [Dwyer et al. Biochemistry 2003, 42:4945-4953] .
  • N-helices in a spike thereby preventing docking of the endogenous C-helices and, hence, formation of the native 6- helix bundle, the latter being a requisite for membrane fusion
  • trimeric alpha-helical coiled coils have the potential to bind to (associate with) peptidic fragments in a strong and specific manner, e.g., in a configuration wherein the bound fragments are strictly alpha-helical and/or are oriented antiparallel to the coiled coil helices and/or are tightly side chain-anchored into the grooves formed by adjacent coiled coil helices and/or are tightly hydrogen-bonded (H-bonded) to the coiled coil helices and/or make tight electrostatic interactions with the coiled coil helices.
  • the experimentally determined structures of viral fusion proteins provide a source of structural information that may be utilized in the design of trimeric alpha-helical coiled coil structures for the purpose of binding target peptides or proteins.
  • Possible current and future embodiments of the present invention relate to designed (artificial, non- natural) trimeric alpha-helical coiled coils that are capable of binding selectively to target peptides or proteins.
  • such designed coiled coil constructs bind to peptide molecules, either free in solution or attached to a solid support.
  • such designed coiled coil constructs bind to a linear fragment in a protein; examples of the latter type of binding include, without limitation, binding to intrinsically disordered protein (IDP) fragments [reviewed in Hansen et al . J Biol Chem 2006, 281:1853-1856], flexible protein loops or tail fragments [Dunker et al . PDB Newsletter 1997, 81:3-5], or transiently disordered protein fragments, e.g. an intermediate during a viral fusion process [Koshiba and Chan J Biol Chem 2003, 278:7573-7579] .
  • IDP intrinsically disordered protein
  • a designed coiled coil construct can bind to a folded protein, for example, a protein of known tertiary structure displaying a set of surface amino acid residues in a configuration that is structurally compatible with the surface of the designed coiled coil construct.
  • the following non-standard method exploits some of the characteristics that are unique to trimeric coiled coils (e.g., the availability of structural information in the Protein Data Bank, the trimeric nature of the scaffold structures, experimental data on protein fragments in association with trimeric coiled coils, and the like) and is therefore considered a preferred, though not obligatory, design method.
  • a method to generate a composition of artificial peptides forming subjects of the present invention includes the steps of
  • step 1 providing a reference 3-D structural representation of a triple-stranded, parallel, alpha-helical coiled coil complex by retrieving the corresponding atomic coordinates from the Protein Data Bank;
  • step 2 providing a set of 3-D structural representations of triple-stranded, parallel, alpha-helical coiled coil complexes that are associated with additional proteinaceous elements, by retrieving the corresponding atomic coordinates from the Protein Data Bank;
  • step 3 superimposing one or more of the representations of step (2) onto the representation of step (1) by applying a least-squares fitting method to a portion or all of the backbone atoms of the coiled coil regions of the representations of steps (1) and (2);
  • step 4 selecting, from coiled coil regions of representations of step (2), amino acid residues that are in contact with proteinaceous chemical groups, for example, side-chain or backbone chemical groups; (step 5) in silico grafting, by way of transferring atomic coordinates, either the entire amino acid residues selected in step (4), or only their side-chains, onto the reference 3-D structural representation of step (1), and, optionally, optimizing the conformation of the grafted amino acid residues by using a suitable molecular modeling method, for example, an energy minimization method or a molecular dynamics method;
  • a suitable molecular modeling method for example, an energy minimization method or a molecular dynamics method
  • step 6 formulating a final composition of artificial peptides by way of synthesizing peptides having an amino acid sequence as appearing in the reference representation of step (1) being substituted into amino acid residues selected in step (4) and grafted in step (5) ;
  • step 7 measuring the binding affinity of the composition of artificial peptides of step (6) for one or more peptides having amino acid residues that are structurally compatible with the binding surface of said artificial peptides, said measurement serving to identify true-positive and false- positive binders.
  • true-positive binders are predicted binders that are experimentally confirmed, whereas false-positive binders are experimentally disproved.
  • theoretical methods e.g., steps 1 - 6 of said workable method
  • steps 1 - 6 of said workable method can considerably expedite identification of true binders by formulating a limited number of potential binders that can be experimentally tested (e.g., by step 7 of said workable method) .
  • a very strong binding is defined as a binding that is characterized by a dissociation constant (Kd) of about 1 nanomolar, good
  • binding specificity is related to binding affinity by the simple rule ⁇ the higher the affinity, the higher the specificity' [Eaton et al . Chem Biol 1995, 2:633-638] .
  • an important aspect of the present invention is that high binding specificity of the artificial coiled coil peptides for their target compound is not preferred and, therefore, a high binding affinity is also not a requirement.
  • the latter is due to a number of potential applications of the present invention.
  • artificial coiled coil peptides are acquired which recognize (show detectable binding to) target molecules displaying a given surface pattern (surface motif, critical residues of a binding site) . It may be advantageous that said coiled coil peptides also recognize other target molecules displaying the same, or a similar, surface pattern, this phenomenon being generally known as ⁇ cross-reactivity' or ⁇ cross-binding' . Cross-reactivity is one of the main consequences of low specificity and can be a favorable or unfavorable property, depending on the goal of the application .
  • An important application of the present invention may be to acquire artificial coiled coil peptides which show detectable cross-reactivity with a variety of target molecules.
  • Such type of reactivity binding, recognition
  • the binding primarily depends on these critical residues and not on other residues of the surface pattern.
  • the said coiled coil peptides will have an inherent potential to recognize a variety of different target molecules that are essentially unrelated in amino acid sequence, tertiary structure and biological function.
  • a preferred application of the present invention is to use artificial coiled coil peptides to screen for (detect, by way of binding to, ) target molecules of different nature and function, while the latter share essentially only a number of highly similar critical amino acid residues or, in general, proteinaceous chemical groups.
  • 'peptidic fragment' preferred instances of critical residues are embodied by series of specific amino acid residues occurring within said peptidic fragment, such series of specific residues also being referred to as 'sequence motifs' or 'sequence patterns' .
  • a sequence motif may be formally noted (encoded, represented) as a pseudo-amino acid sequence wherein critical residues are symbolized by standard amino acid one-letter codes, non-critical residues by "x" characters, and flanking fragments by "-" signs.
  • a specific sequence motif could be "-IxxLxxxV-", meaning that the "I”, “L” and “V” characters represent critical isoleucine, leucine and valine residues, respectively, the "x” characters represent non-critical residues and the "-” signs represent flanking fragments; according to standard amino acid naming conventions, the mentioned sequence motif would embody all possible peptide sequences having isoleucine (I) followed by two undefined (indifferent) residues, followed by leucine (L) , followed by three undefined residues, followed by valine (V) .
  • a specific sequence motif may be encoded as a pseudo-amino acid sequence wherein critical residues with highly similar physico-chemical properties (e.g., aliphatic, aromatic, positively/negatively charged residues) are grouped and jointly referenced by a suitably chosen symbol.
  • a specific sequence motif of this kind could be "- axxaxxxa-", wherein it is further specified that the characters "a” denote aliphatic residues of the set ⁇ leucine, isoleucine, valine ⁇ , this pseudo-sequence embodying all possible peptide sequences having three aliphatic residues that are spaced as specified in the motif.
  • any particular sequence motif comprising at least two critical residue positions at which maximally four amino acid residues are considered, and which are spaced by a fixed number of non-critical residues, can be genuinely called a specific sequence motif.
  • artificial coiled coil peptides binding selectively to peptidic fragments comprising such sequence motif can be attributed a certain degree of specific binding.
  • absolute or high specificity will generally be not aspired and will in many practical cases not even be desired.
  • ⁇ protein target' preferred instances of critical residues are embodied by series of specific amino acid residues occurring at the molecular surface of said protein target, such series of specific residues also being referred to as 'surface motifs' or 'surface patterns' ; a surface motif cannot be formally noted in pseudo-amino acid sequence format as it embodies a series of critical residues that are disjunct in sequence but clustered in 3-D space.
  • a surface motif is further specified as a set of residues at the surface of a target protein that are critical for binding, generally a subset of the residues forming the full binding site.
  • a surface motif also bears strong similarity to antibody combining sites known in the field as conformational epitopes. Similar to peptidic target fragments, critical residues can either be single amino acid residues or groups thereof.
  • a surface pattern can therefore include a certain degree of diversity while still being envisaged as a specific surface motif. Accordingly, artificial coiled coil peptides binding selectively to protein targets comprising such surface motif can be attributed a certain degree of specific binding. It is also remarked in this context that absolute or high specificity will generally be not aspired and will in many practical cases not even be desired.
  • alanine-scanning alanine-scanning
  • Ala-mutants single-residue alanine-mutants
  • Alanine-mutants showing significantly reduced affinity are indicative of the importance of the wild type amino acid at the corresponding position. Because there exist different human interpretations of what is to be considered a significant reduction in affinity, the latter is specified in a preferred way, as follows.
  • the corresponding wild type residue is deemed critical for the binding.
  • the binding affinity of an Ala-mutant is at least a factor 10 lower (i.e., the dissociation constant, Kd, is at least a factor 10 higher) than that of the wild type compound.
  • the corresponding wild type residue is deemed highly critical. In the other cases (i.e., when the affinity decreases by less than a factor 10, or when it increases), the corresponding wild type residue is deemed not critical.
  • the critical nature of target amino acid residues is demonstrated by comparing the affinity of the unmodified target compound with the affinities of alanine point mutant compounds, or glycine point mutant compounds if the unmodified compound has alanine at the corresponding position.
  • specific amino acid residues of the target compound are deemed critical if the dissociation constant of the corresponding point mutant is at least a factor 10 higher than that of the unmodified target compound. In another, equally preferred possible embodiment, specific amino acid residues of the target compounds are further deemed highly critical if the dissociation constant of the corresponding point mutant is at least a factor 100 higher than that of the unmodified target compound.
  • binding of the same composition of artificial coiled coil peptides is demonstrated for at least two, and preferably multiple (e.g., 10) different target compounds with identical, or physico-chemically highly similar, critical amino acid residues, said demonstrated binding being indicative of a broad applicability of the same artificial coiled coil peptides for recognition of different target compounds sharing essentially only a small number of highly similar critical amino acid residues.
  • any newly discovered chemical or biomolecular compound showing appreciable binding to a given target compound has a certain potential to become a drug lead compound; it may be transformed into a true drug after intensive pharmacokinetic and pharmacodynamic analysis and modifications known as lead optimizations.
  • lead optimizations There are two aspects in this which directly and indirectly relate to the present invention, respectively. The first is about the discovery process, and directly relates to the present invention. (The second aspect is about lead optimization and is further detailed below.) Drug lead discovery tradionally involves brute-force high-throughput screening (HTS) of large libraries of compounds.
  • HTS high-throughput screening
  • An important aspect of 'smart screening' is the design of screening libraries with an improved hit rate.
  • molecular target compounds it would be advantageous to possess small screening libraries with a high content of potential binders. It would be most advantageous to not have to screen a library at all, but to be able to select candidate binders on basis of their previously demonstrated binding properties, for example, a demonstrated capability to bind to target molecules displaying a given sequence pattern or surface pattern.
  • candidate binder if the target compound of interest displays not any sequence or surface pattern that matches with the previously demonstrated binding characteristics of compounds in possession.
  • the second aspect relating to drug development concerns techniques for lead optimization relates only indirectly to the present invention.
  • the discovery of an initial binder to a particular target of interest does not necessarily imply that this binder will become a true drug.
  • initial hits have to be modified (i.e., changed in 'chemical space' for small-molecule compounds or in
  • these artificial peptides and derivatives may be modified, e.g., to enhance the correctness of their folded state; • these artificial peptides and derivatives may be modified, e.g., to enhance their binding affinity to a target compound;
  • these artificial peptides and derivatives may be modified, e.g., to enhance their binding specificity for a target compound
  • these artificial peptides and derivatives may be modified, e.g., to enhance their solubility
  • these artificial peptides and derivatives may be covalently linked to one another by utilizing suitable linker fragments connecting the C-terminal end of one peptide to the N-terminal end of another peptide, this covalent linkage leading to the construction of a single- chain derivative; • these artificial peptides and derivatives may be covalently linked to one another by substituting selected amino acid residues for cysteine, e.g., to stabilize their folded structure by disulfide bonds;
  • these artificial peptides and derivatives may be covalently linked to protein molecules, e.g., they may be incorporated in fusion proteins;
  • these artificial peptides and derivatives may be covalently linked to other copies of the same artificial peptides or derivatives, e.g., to increase avidity; • these artificial peptides and derivatives may be covalently linked to other artificial peptides or derivatives with different binding properties, e.g., to provide bi- or multispecificity;
  • constructs would be highly desirable because they may allow production via standard molecular biological (recombinant) techniques. Furthermore, such constructs may considerably facilitate the development of coiled coils comprising asymmetric (non-identical) alpha- helical fragments, which opens the way to a variety of novel applications. The formation of the coiled coil region would not involve association of free peptides but folding of a single chain which may, or may not, be thermodynamically advantageous .
  • the linker fragment can also be used to supplement the scaffold structure with additional desired properties including, but not limited to, further stabilization of the construct, epitope presentation, immunological masking, crosslinking, labeling, etc.
  • additional desired properties including, but not limited to, further stabilization of the construct, epitope presentation, immunological masking, crosslinking, labeling, etc.
  • the connection of opposite (distal) ends in a protein tertiary structure is far from trivial. It is has not yet been demonstrated how long such linker fragments should be to connect the alpha-helical termini in a suitable (intended) way, e.g., to facilitate, or at least permit, association of the alpha-helical fragments with the proper spatial arrangement (handedness around the central axis) .
  • Example 1 Amino acid sequence of an artificial peptide with core and non-core residues.
  • This example provides the amino acid sequence of a specific peptide forming an instance of the present invention.
  • the amino acid sequence, AIAAIQKQIAALQKQIAAIQKQIA is presented in single-letter notation, wherein A refers to alanine, I to isoleucine, L to leucine, Q to glutamine, and K to lysine.
  • the peptides with this amino acid sequence fold in solution into triple-stranded, parallel, alpha-helical coiled coil complexes by way of their isoleucine and leucine amino acid residues forming a hydrophobic core (center, interior) and the other residues being oriented towards solvent.
  • the artificial peptide comprises three heptad repeats labeled "HRl", "HR2" and "HR3" in Figure 1.
  • the Figure 1 is a schematic representation of the amino acid sequence of an artificial peptide comprising heptad repeats
  • the peptide further comprises a C-terminal heptad core residue labeled "t”.
  • the peptide further comprises N- and C-terminal flanking fragments labeled "N" and "C”, respectively.
  • Each heptad repeat residue is further annotated with indices "a” to "g” and a number corresponding to the heptad repeat number.
  • Core residues are located at a- and d-positions. It is seen that 5 out of the 6 core residues of the three full heptad repeats are isoleucines.
  • the isoleucine residue labeled "a4" belongs to the partial heptad repeat "t”.
  • Example 2. Principles of a triple-stranded, parallel, alpha- helical coiled coil complex.
  • Heptad core residues are shielded from solvent in triple- stranded, parallel, alpha-helical coiled coil complexes, as illustrated in Figure 2.
  • Non-covalent interactions between contacting core residues provide the main thermodynamic driving force for the peptides to adopt such fold.
  • the Figure 2 is a helical wheel representation of a triple-stranded, parallel, alpha-helical coiled coil scaffold.
  • the left panel shows a top view on the scaffold.
  • the right panel shows a linear sequence of heptad repeat positions. Only one heptad repeat is displayed for clarity reasons. Different shades are used to indicate specific topological positions.
  • the non-core residues are at least partially solvent- accessible (positions E, G less than B, C, and positions B, C less than F) and are susceptible to amino acid substitutions without (major) implications for the stability of the complex (scaffold structure) .
  • Example 3 Alpha-helical structure and reversible folding/unfolding.
  • the inventors have synthesized the peptide with the amino acid sequence Ac-MSIEEIQKQQAAIQKQIAAIQKQIYRMTP-NH2 and recorded the circular dichroism (CD) spectrum.
  • the amino acid sequence is given in single-letter code; Ac- and -NH2 mean that the peptide was acetyl-initiated and amide-terminated, respectively.
  • This peptide is to be considered as a derivative of the reference peptide composed of the triple heptad repeat sequence (IAAIQKQ) 3, with modifications at the amino- (N-) and carboxy- (C-) terminal ends to improve the alpha-helical nature of the termini (often referred to as capping) . More specifically, the flanking residues Ac-MS- were attached at the N-terminus, in combination with the substitution of two consecutive glutamic acid residues (EE) for the two alanine residues (AA) in the first heptad of the reference sequence.
  • EE glutamic acid residues
  • flanking residues -IYRMTP-NH2 were attached at the C-terminus, such that the amino acids isoleucine (I) and methionine (M) are located at conventional heptad a- and d-positions, allowing this flanking sequence to form an extra, though incomplete, heptad.
  • the tyrosine (Y) was introduced at a solvent-oriented b-position to enable spectrophotometry concentration determination.
  • the arginine (R), threonine (T) and proline (P-NH2) residues were introduced to improve C- terminal helical capping.
  • isoleucine (I) residue at the a-position of the second heptad was replaced by a glutamine (Q) residue to force the coiled coil-forming peptides to associate in the correct (intended) way, i.e., to ascertain formation of a trimeric complex and to avoid possible heptad register shifts [Eckert et al . J MoI Biol 1998, 284:859-865] .
  • the said synthesized peptide was dissolved at a concentration of 292 microM in 20 mM phosphate buffer (PBS), 150 mM NaCl, pH 7.2.
  • the CD spectra were measured between 200 and 250 nM, at 5 and 90 degrees Celsius ( Figure 3) .
  • the spectrum at 5 degrees Celsius was indicative of a high alpha-helical secondary structure content, in agreement with the expectation that all heptad regions, but not all of the flanking residues, would assemble as alpha-helical coiled coils.
  • the spectrum at 90 degrees Celsius showed that the alpha-helical structure was greatly, but not completely, lost at elevated temperatures.
  • T 1 the transition temperature, where 50% of the total peptide concentration is associated
  • Figure 5 represents fitting of a theoretic equation for trimeric association to experimental data.
  • the experimental data are taken from Figure 4, curve labeled "UP”.
  • the theoretic equations used are listed supra.
  • the fitted parameters (fitting results) are listed at the right in Figure 5.
  • Transit. T corresponds to T t , but is expressed here in degrees Celsius.
  • the parameter “delta C p " was kept constant at 3.0 kJ mol "1 K “1 .
  • the parameters "theta M (T)” and “theta T (T)” were treated as linear functions of T, resulting in the white straight lines described by the respective offsets and slopes indicated at the right in the figure.
  • RMS Resid refers to the root-mean-square of the differences between experimental and theoretic data points.
  • the fitted (theoretic) curve itself is plotted in white on the figure and coincides over the entire temperature range with the experimental data points shown in black.
  • Figure 6 shows the thermal denaturation curve for a sample preparation of the Q2al peptide under the same conditions as in Example 3.
  • the global CD signal was somewhat lower than expected, which could be due to an instrumental deviation, an error in the concentration determination, a lower purity, or a lower than expected alpha-helical content.
  • the main goal of this experiment was to examine the effect of the glutamine-to-isoleucine mutant on the stability of the complex. It was therefore interesting to find that this variant showed extremely high resistance against thermal denaturation, i.e., it was extremely thermostable.
  • the estimated transition temperature was around 97 degrees Celsius, although the latter was difficult to determine because of incompleteness of the transition. Also, the down- scan showed full recovery of the CD signal, indicating full reversibility.
  • UV ultraviolet
  • RI refractive index
  • SLS static light scattering
  • Example 3 To further analyse the tolerance of the trimeric coiled coil scaffold towards amino acid residue substitutions at specific core positions, the following mutants of the reference peptide examined in Example 3 (i.e., the one comprising a glutamine at position 2a, not the more stable Q2al mutant of Example 4) were synthesized: 3aQ, 3aL, 3aV, 3aA, 3aS, 3dQ, 3dL, 3dV, 3dA and 3dS, wherein each time “3” refers to the third heptad and "a” and “d” refer to a- and d-positions, respectively; the letters Q, L, V, A and S refer to mutations into glutamine, leucine, valine, alanine and serine, respectively.
  • isoleucine is a highly preferred core residue.
  • the amino acid proline is known to be structurally disruptive in alpha-helices. Glycine has a very low alpha-helical propensity but is generally not disruptive. All other residue types are compatible with alpha-helices but each have a different helical propensity. Moreover, it has been demonstrated that particular non-core residues, especially at e- and g-positions can significantly influence the stability of a coiled coil, at least in dimers but likely also in trimeric complexes [Yu Adv Drug Deliv Rev 2002, 54:1113-1129] .
  • the moderately stable reference peptide Q2a (with glutamine at core position 2a) was selected as a practically more suitable context.
  • leucine (L) , tryptophan (W) , glutamic acid (E) and arginine (R) were selected as representative aliphatic, aromatic, negatively charged and positively charged amino acids, respectively; the latter amino acids should preferably be tolerated by the scaffold.
  • control amino acid proline was selected, which should be disruptive if the scaffold structure folds in the way as intended.
  • the said amino acid residue types were substituted at the non-core positions b and c of the third heptad (i.e., at positions 3b and 3c) in peptide Q2a.
  • the list of selected amino acids was further amended for testing mutability at e- and g-positions in the second heptad (i.e., at positions 2e and 2g) in peptide Q2a. At these positions, the amino acids glycine (G) , serine (S) , tyrosine (Y) , asparagine (N) and aspartic acid (D) were also tested.
  • Figure 10 shows the experimentally determined transition temperatures (bars) for the tested point and double mutants.
  • the mutants are denoted by the position of the mutation followed by the mutant residue type in single-letter notation
  • Double mutants are denoted by the modified heptad, followed by the modified positions, followed by the mutant single-letter residue types at the respective positions (for example, "2egRD” indicates arginine at 2e and aspartic acid at 2g) .
  • Mutants labeled by a single asterisk (*) were not determined because they could not be synthesized to sufficient purity.
  • Mutants labeled by a double asterisk (**) were highly unstable, having transition temperatures presumably below -35 0 C, and the corresponding values were fixed at this value.
  • the double mutations have a largely, though not completely, additive effect.
  • the two double mutants comprising the strongly destabilizing 2eD substitution (2egDR and 2egDD) are also the two least stable double mutants, but 2egDR has a higher transition temperature than 2eD despite the moderately unfavorable effect of 2gR.
  • pairwise electrostatic (charge-charge, ionic, Coulombic) interactions play some additional role in the double e,g-mutants, as can also be inferred from the other double mutants 2egRD, 2egRE, 2egER.
  • preferred embodiments of the present invention relate to scaffolds lacking such interactions. More specifically, preferred embodiments of the present invention relate to trimeric scaffolds comprising heptad repeats which have glutamine at e- and g-positions, as is the case in the tested Q2a and Q2I reference scaffolds.
  • a representative number of amino acid substitutions at characteristic non-core positions were tested in a trimeric coiled coil scaffold: 1 amino acid (lysine) at the very exposed f-position, 5 at the largely exposed b- and expositions, and 10 at the moderately exposed e- and g- positions.
  • 1 amino acid (lysine) at the very exposed f-position
  • 5 at the largely exposed b- and expositions
  • 10 at the moderately exposed e- and g- positions.
  • the more buried an amino acid is in a certain tertiary structure, the more interactions it makes with the remainder of the structure, and the more critical its nature (and changes therein) will be with respect to the stability of the tertiary structure.
  • the more exposed (solvent-oriented) an amino acid the less critical will be its identity in the sense that mutations at this position will be better tolerated by (have a lower impact on) the tertiary structure.
  • preferred embodiments of the present invention relate to scaffold molecules formed by reference peptides Q2a and Q2al, wherein one or more of the non-core amino acids are substituted into another amino acid type than present in the reference peptides.
  • One particular scaffold variant namely the trimeric coiled coil having all-alanine at the non-core positions b, c, e, f and g, forms a special case, in that, it represents the essence of what is generally understood by a scaffold molecule, i.e., a molecule that acts as a carrier of chemical groups.
  • All natural amino acids (except proline) have the same backbone (main chain) atoms, but differ in the composition of their side chains.
  • all natural amino acids have at least one carbon atom (beta carbon, C-beta, CB) to which the remainder of the side-chain atoms are attached.
  • Alanine only has a (hydrogen-saturated) beta carbon atom.
  • Other amino acids are thus formally alanines wherein particular chemical groups are attached to the beta carbon atom.
  • alanine represents the ⁇ chemically pure' instance of a carrier amino acid
  • proteins displaying alanines at their surface form ⁇ chemically pure' instances of scaffold molecules onto which other side-chain types can be attached.
  • a most preferred (because chemically pure) embodiment of the present invention relates to a trimeric coiled coil scaffold wherein all non-core amino acids are alanines. Because of the intrinsically high mutability of non- core amino acids, as demonstrated in the present example, other preferred embodiments of the present invention relate to variants of the latter scaffold wherein one or more of the non-core amino acids are substituted into another amino acid type than alanine.
  • biotin and c-myc tags were attached to the N- and C-termini, respectively, of both the reference peptide of Example 3, here named Q2a, and the mutant peptide of Example 4, Q2al.
  • a small serine-glycine spacer fragment was placed in between the tags and the peptides on either side.
  • tagged Q2a had the sequence biotin-SGMS IEEIQKQQAAIQKQIAAIQKQIYRMTPSGEQKLI SEEDL-NH2 and tagged Q2al had the sequence biotin-SGMS IEEIQKQIAAIQKQIAAIQKQIYRMTPSGEQKLI SEEDL-NH2.
  • the two peptides were immobilized through the biotin moiety on a neutravidin-coated plate, and the availability of the c-myc tag was tested using a mouse anti-c-myc primary antibody and an anti-mouse horseradish peroxidase (HRP) conjugate as secondary detection system.
  • HRP horseradish peroxidase
  • the untagged peptides were also tested as negative controls. As an additional negative control, the same experiments were performed using non-coated plates. Skimmed milk was used as blocking agent.
  • Figure 11 shows positive detection of the tagged peptides, no detection of untagged peptides, and no detection of peptides on non-coated plates. Said positive detection was found to be independent of the concentration of tagged peptides.

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Abstract

La présente invention concerne un échafaudage protéique non naturel thermodynamiquement stable constitué de trois peptides associés de manière non covalente. Selon l'invention, chaque séquence peptidique comprend moins de cinquante résidus d'acides aminés et au moins 50 % desdits résidus sont des acides aminés substituables par au moins dix types de résidus d'acides aminés différents. La présente invention concerne également un échafaudage non naturel, en spirale alpha-hélicoïdale parallèle à trois brins, selon lequel chacune des trois séquences peptidiques constitutives comprend entre 2 et 7 répétitions d'heptades, au moins 50 % des résidus centraux étant des isoleucines, tous les résidus non centraux étant des alanines et les séquences peptidiques constitutives restant associées dans des conditions physiques qui diffèrent significativement des conditions physiologiques.
PCT/EP2008/061886 2007-09-07 2008-09-08 Echafaudage protéique non naturel constitué de trois peptides associés de manière non covalente WO2009030780A2 (fr)

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US12/676,783 US9217011B2 (en) 2007-09-07 2008-09-08 Non-natural proteinaceous scaffold made of three non-covalently associated peptides
AT08803854T ATE538129T1 (de) 2007-09-07 2008-09-08 Nicht natürliches proteinöses gerüst aus drei nicht kovalent assoziierten peptiden

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ATE538129T1 (de) 2012-01-15
US9217011B2 (en) 2015-12-22
US20100305304A1 (en) 2010-12-02

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